Journal ArticleDOI
Progress in tracing the evolutionary paths of cytochrome P450.
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TLDR
The value of synteny across genomes is emphasized as a tool for deep time evolutionary studies of P450s in animals and there is evidence that macrosynteny may be useful in tracing the origin of animal CYP clans.About:
This article is published in Biochimica et Biophysica Acta.The article was published on 2011-01-01. It has received 198 citations till now. The article focuses on the topics: Synteny.read more
Citations
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Journal ArticleDOI
A P450-centric view of plant evolution.
TL;DR: Comparative analysis of the plant CYPomes provides information on the successive steps required for the evolution of land plants, and points to several cases of convergent evolution in plant metabolism.
Journal ArticleDOI
Cytochrome P450 monooxygenases: an update on perspectives for synthetic application.
Vlada B. Urlacher,Marco Girhard +1 more
TL;DR: A short up-to-date overview of recent results on P450 engineering for technical applications including aspects of whole-cell biocatalysis with engineered recombinant enzymes and recently identified P450s with novel biotechnologically relevant properties are given.
Journal ArticleDOI
Genome sequence of the model medicinal mushroom Ganoderma lucidum
Shilin Chen,Jiang Xu,Chang Liu,Yingjie Zhu,David R. Nelson,Shiguo Zhou,Chunfang Li,Lizhi Wang,Xu Guo,Yongzhen Sun,Hongmei Luo,Ying Li,Jingyuan Song,Bernard Henrissat,Anthony Levasseur,Jun Qian,Jianqin Li,Xiang Luo,Linchun Shi,Liu He,Li Xiang,Xiaolan Xu,Yunyun Niu,Qiushi Li,Mira V. Han,Haixia Yan,Jin Zhang,Haimei Chen,Aiping Lv,Zhen Wang,Mingzhu Liu,David C. Schwartz,Chao Sun +32 more
TL;DR: The sequence analysis reveals an impressive array of genes encoding cytochrome P450s (CYPs), transporters and regulatory proteins that cooperate in secondary metabolism, making this organism a potential model system for the study of secondary metabolic pathways and their regulation in medicinal fungi.
Journal ArticleDOI
Carlactone is converted to carlactonoic acid by MAX1 in Arabidopsis and its methyl ester can directly interact with AtD14 in vitro
Satoko Abe,Aika Sado,Kai Tanaka,Takaya Kisugi,Kei Asami,Saeko Ota,Hyun Il Kim,Kaori Yoneyama,Xiaonan Xie,Xiaonan Xie,Toshiyuki Ohnishi,Yoshiya Seto,Shinjiro Yamaguchi,Kohki Akiyama,Koichi Yoneyama,Koichi Yoneyama,Takahito Nomura,Takahito Nomura +17 more
TL;DR: It is shown that CL is converted into a carboxylated metabolite, named carlactonoic acid, byArabidopsis MAX1, the enzymatic function of which had been unknown, and that its methyl ester has the ability to interact with a SL receptor and suppress shoot branching in Arabidopsis.
Journal ArticleDOI
The evolution and pathogenic mechanisms of the rice sheath blight pathogen
Aiping Zheng,Runmao Lin,Danhua Zhang,Peigang Qin,Lizhi Xu,Peng Ai,Lei Ding,Yanran Wang,Yao Chen,Yao Liu,Zhigang Sun,Haitao Feng,Xiaoxing Liang,Rongtao Fu,Changqing Tang,Qiao Li,Jing Zhang,Zelin Xie,Qiming Deng,Shuangcheng Li,Shiquan Wang,Jun Zhu,Lingxia Wang,Huainian Liu,Ping Li +24 more
TL;DR: The draft genome sequence of the rice sheath blight disease pathogen, R. solani AG1 IA, is assembled using next-generation Illumina Genome Analyser sequencing technologies and reveals the exclusive expression patterns of the pathogenic determinants during host infection.
References
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Journal ArticleDOI
The Pfam protein families database
Marco Punta,Penny Coggill,Ruth Y. Eberhardt,Jaina Mistry,John Tate,Chris Boursnell,Ningze Pang,Kristoffer Forslund,Goran Ceric,Jody Clements,Andreas Heger,Liisa Holm,Erik L. L. Sonnhammer,Sean R. Eddy,Alex Bateman,Robert D. Finn +15 more
TL;DR: The definition and use of family-specific, manually curated gathering thresholds are explained and some of the features of domains of unknown function (also known as DUFs) are discussed, which constitute a rapidly growing class of families within Pfam.
Journal ArticleDOI
P450 superfamily: Update on new sequences, gene mapping, accession numbers and nomenclature
David R. Nelson,Luc Koymans,Tetsuya Kamataki,John J. Stegeman,Ren Feyereisen,David J. Waxman,Michael R. Waterman,Osamu Gotoh,Minor J. Coon,Ron W. Estabrook,Irwin C. Gunsalus,Daniel W. Nebert +11 more
TL;DR: This revision supersedes the four previous updates in which a nomenclature system, based on divergent evolution of the P450 superfamily has been described and is similar to that proposed in the previous updates.
Journal ArticleDOI
The amphioxus genome and the evolution of the chordate karyotype
Nicholas H. Putnam,Thomas Butts,David E. K. Ferrier,Rebecca F. Furlong,Uffe Hellsten,Takeshi Kawashima,Takeshi Kawashima,Marc Robinson-Rechavi,Marc Robinson-Rechavi,Eiichi Shoguchi,Eiichi Shoguchi,Astrid Terry,Jr-Kai Yu,E grave,lia Benito-Gutiérrez,Inna Dubchak,Jordi Garcia-Fernàndez,Jeremy J. Gibson-Brown,Igor V. Grigoriev,Amy C. Horton,Pieter J. de Jong,Jerzy Jurka,Vladimir V. Kapitonov,Yuji Kohara,Yoko Kuroki,Erika Lindquist,Susan Lucas,Kazutoyo Osoegawa,Len A. Pennacchio,Asaf Salamov,Yutaka Satou,Tatjana Sauka-Spengler,Jeremy Schmutz,Tadasu Shin-I,Atsushi Toyoda,Marianne Bronner-Fraser,Asao Fujiyama,Linda Z. Holland,Peter W. H. Holland,Nori Satoh,Nori Satoh,Daniel S. Rokhsar,Daniel S. Rokhsar +42 more
TL;DR: Whole-genome comparisons illuminate the murky relationships among the three chordate groups (tunicates, lancelets and vertebrates), and allow not only reconstruction of the gene complement of the last common chordate ancestor but also partial reconstruction of its genomic organization.
Journal ArticleDOI
Fungal secondary metabolism — from biochemistry to genomics
TL;DR: Questions are addressed, including which evolutionary pressures led to gene clustering, why closely related species produce different profiles of secondary metabolites, and whether fungal genomics will accelerate the discovery of new pharmacologically active natural products.
Journal ArticleDOI
A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea.
Dongying Wu,Dongying Wu,Philip Hugenholtz,Konstantinos Mavromatis,Rüdiger Pukall,Eileen Dalin,Natalia Ivanova,Victor Kunin,Lynne Goodwin,Martin Wu,Brian J. Tindall,Sean D. Hooper,Amrita Pati,Athanasios Lykidis,Stefan Spring,Iain Anderson,Patrik D'haeseleer,Patrik D'haeseleer,Adam Zemla,Mitchell Singer,Alla Lapidus,Matt Nolan,Alex Copeland,Cliff Han,Feng Chen,Jan Fang Cheng,Susan Lucas,Cheryl A. Kerfeld,Elke Lang,Sabine Gronow,Patrick S. G. Chain,Patrick S. G. Chain,David Bruce,Edward M. Rubin,Nikos C. Kyrpides,Hans-Peter Klenk,Jonathan A. Eisen,Jonathan A. Eisen +37 more
TL;DR: The results strongly support the need for systematic ‘phylogenomic’ efforts to compile a phylogeny-driven ‘Genomic Encyclopedia of Bacteria and Archaea’ in order to derive maximum knowledge from existing microbial genome data as well as from genome sequences to come.
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